NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q03172 UniProt NPD GO	ZEP1_MOUSE	Zinc finger protein 40 (Transcription factor alphaA-CRYBP1) (Alpha A-crystallin-binding protein I) ( ...	0.98	+	nuc	0	Nucleus	nucleus [IDA]			2688
Q9P243 UniProt NPD GO	ZN406_HUMAN	Zinc finger protein 406 (Protein ZFAT)	0.98	-	nuc	0	Nucleus (Potential)				1243
Q6AHZ1 UniProt NPD GO	ZN518_HUMAN	Zinc finger protein 518	0.98	+	nuc	0	Nucleus (Probable)				1483
Q9H0D2 UniProt NPD GO	ZN541_HUMAN	Zinc finger protein 541	0.98	+	nuc	0	Nucleus (By similarity)				792
Q4R2Z8 UniProt NPD GO	ZN541_MACFA	Zinc finger protein 541	0.98	+	nuc	0	Nucleus (By similarity)				803
Q61464 UniProt NPD GO	ZN638_MOUSE	Zinc finger protein 638 (Nuclear protein 220) (Zinc-finger matrin-like protein)	0.98	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				1960
Q96JP5 UniProt NPD GO	ZFP91_HUMAN	Zinc finger protein 91 homolog (Zfp-91)	0.98	+	nuc	0	Nucleus				570
Q00947 UniProt NPD GO	STP1_YEAST	Zinc finger protein STP1	0.98	+	nuc	0	Nucleus	nucleus [IDA]			577
Q8CCH7 UniProt NPD GO	FOG2_MOUSE	Zinc finger protein ZFPM2 (Zinc finger protein multitype 2) (Friend of GATA protein 2) (Friend of GA ...	0.98	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			1151
Q9W4T0 UniProt NPD GO	PDE4D_DROME	cAMP-specific 3',5'-cyclic phosphodiesterase, isoform M (EC 3.1.4.17) (Learning/memory process prote ...	0.98	-	mit	0					903
Q02825 UniProt NPD GO	SEN54_YEAST	tRNA-splicing endonuclease subunit SEN54 (tRNA-intron endonuclease SEN54) (Splicing endonuclease of ...	0.98	-	nuc	0	Nucleus. Intracellular membrane; peripheral membrane protein. Mitochondrion; mitochondrial outer mem ...	mitochondrial outer membrane [IDA] nuclear inner membrane [TAS] tRNA-intron endonuclease complex [TAS]			467
P34756 UniProt NPD GO	FAB1_YEAST	1-phosphatidylinositol-3-phosphate 5-kinase FAB1 (EC 2.7.1.150) (Phosphatidylinositol-3-phosphate 5- ...	0.97	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein. Endosome; endosomal membrane; peripheral me ...	mitochondrion [IDA] vacuolar membrane [TAS]			2278
Q99JE6 UniProt NPD GO	PLCB3_RAT	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3 (EC 3.1.4.11) (Phospholipase C-beta ...	0.97	+	nuc	0	Cytoplasm. Membrane. And particulate fractions	cytosol [IDA] insoluble fraction [IDA]			1234
Q12420 UniProt NPD GO	SNU66_YEAST	66 kDa U4/U6.U5 small nuclear ribonucleoprotein component	0.97	+	nuc	0	Nucleus	U4/U6 x U5 tri-snRNP complex [IDA]			587
P40574 UniProt NPD GO	YAP5_YEAST	AP-1-like transcription factor YAP5	0.97	+	nuc	0	Cytoplasm. Nucleus	nucleus [IC]			245
O14617 UniProt NPD GO	AP3D1_HUMAN	AP-3 complex subunit delta-1 (Adapter-related protein complex 3 subunit delta-1) (Delta-adaptin 3) ( ...	0.97	+	nuc	0		Golgi apparatus [TAS]	607246		1153
Q09811 UniProt NPD GO	HUS2_SCHPO	ATP-dependent DNA helicase hus2/rqh1 (EC 3.6.1.-)	0.97	-	nuc	0	Nucleus	RecQ helicase-Topo III complex [IDA]			1328
Q6BL34 UniProt NPD GO	DBP10_DEBHA	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.97	+	nuc	0	Nucleus; nucleolus (By similarity)				932
Q2UHB7 UniProt NPD GO	DBP4_ASPOR	ATP-dependent RNA helicase dbp4 (EC 3.6.1.-)	0.97	+	nuc	0	Nucleus; nucleolus (By similarity)				796
Q4P9E5 UniProt NPD GO	SPB4_USTMA	ATP-dependent rRNA helicase SPB4 (EC 3.6.1.-)	0.97	-	nuc	0	Nucleus; nucleolus (By similarity)				767
Q8N302 UniProt NPD GO	AGGF1_HUMAN	Angiogenic factor with G patch and FHA domains 1 (Angiogenic factor VG5Q) (Vasculogenesis gene on 5q ...	0.97	+	nuc	0	Cytoplasm. Secreted protein. Cytoplasmic in microvascular endothelial cells. Upon angiogenesis, when ...	cytoplasm [IDA] extracellular region [IDA] perinuclear region [IDA]	608464		714
Q80UU1 UniProt NPD GO	ANKZ1_MOUSE	Ankyrin repeat and zinc finger domain-containing protein 1	0.97	+	nuc	0					748
Q66H85 UniProt NPD GO	ANKZ1_RAT	Ankyrin repeat and zinc finger domain-containing protein 1	0.97	+	nuc	0					722
Q9H8Y5 UniProt NPD GO	ANKZ1_HUMAN	Ankyrin repeat and zinc finger domain-containing protein 1 (Zinc finger protein 744)	0.97	+	nuc	0					726
Q62901 UniProt NPD GO	RERE_RAT	Arginine-glutamic acid dipeptide repeats protein (Atrophin-1-related protein)	0.97	-	nuc	0	Nucleus (By similarity). Localized in nuclear bodies of variables size. Colocalized with PML and BAX ...				1559
Q80TZ9 UniProt NPD GO	RERE_MOUSE	Arginine-glutamic acid dipeptide repeats protein (Atrophin-2)	0.97	+	nuc	0	Nucleus (By similarity). Localized in nuclear bodies of variables size. Colocalized with PML and BAX ...	histone deacetylase complex [IPI]			1558
Q5PPJ2 UniProt NPD GO	RSRC1_RAT	Arginine/serine-rich coiled coil protein 1	0.97	+	nuc	0					334
Q5B993 UniProt NPD GO	ATG11_EMENI	Autophagy-related protein 11	0.97	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Vacuolar and perivacuolar p ...				1371
Q02040 UniProt NPD GO	XE7_HUMAN	B-lymphocyte antigen precursor (B-lymphocyte surface antigen) (721P) (Protein XE7)	0.97	-	nuc	0	Membrane; peripheral membrane protein (Probable)		465000		695
Q8CGN4 UniProt NPD GO	BCOR_MOUSE	BCoR protein (BCL-6 corepressor)	0.97	+	nuc	0	Nucleus				1759
P52963 UniProt NPD GO	E41LA_MOUSE	Band 4.1-like protein 4A (Protein NBL4)	0.97	+	nuc	0					554
Q03368 UniProt NPD GO	BLVR_BOVIN	Bovine leukemia virus cell receptor precursor (BLV-R) (BLVPCP1)	0.97	+	nuc	0	Membrane; single-pass type I membrane protein				843
Q864U1 UniProt NPD GO	BRCA1_BOVIN	Breast cancer type 1 susceptibility protein homolog	0.97	-	nuc	0	Nucleus (Potential)				1849
Q9GKK8 UniProt NPD GO	BRCA1_PANTR	Breast cancer type 1 susceptibility protein homolog	0.97	-	nuc	0	Nucleus (By similarity)	gamma-tubulin ring complex [NAS] nucleus [TAS]			1863
Q6J6J0 UniProt NPD GO	BRCA1_PONPY	Breast cancer type 1 susceptibility protein homolog	0.97	-	nuc	0	Nucleus (Potential)				1863
Q9UIF9 UniProt NPD GO	BAZ2A_HUMAN	Bromodomain adjacent to zinc finger domain 2A (Transcription termination factor I-interacting protei ...	0.97	+	nuc	0	Nucleus; nucleolus. Colocalizes with the basal RNA polymerase I transcription factor UBF in the nucl ...	nucleolus organizer complex [NAS]	605682		1878
Q9ULD4 UniProt NPD GO	BRPF3_HUMAN	Bromodomain and PHD finger-containing protein 3	0.97	-	nuc	0					1205
Q07442 UniProt NPD GO	BDF2_YEAST	Bromodomain-containing factor 2	0.97	+	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]			638
Q8K2F0 UniProt NPD GO	BRD3_MOUSE	Bromodomain-containing protein 3 (Bromodomain-containing FSH-like protein FSRG2)	0.97	+	nuc	0	Nucleus (Potential)				726
O88480 UniProt NPD GO	CABIN_RAT	Calcineurin-binding protein Cabin 1 (Calcineurin inhibitor) (CAIN)	0.97	-	nuc	0	Cytoplasm				2182
Q8SXX4 UniProt NPD GO	CAPON_DROME	Capon-like protein	0.97	+	nuc	0					698
Q9BXF3 UniProt NPD GO	CECR2_HUMAN	Cat eye syndrome critical region protein 2	0.97	+	nuc	0			607576		1484
P04821 UniProt NPD GO	CDC25_YEAST	Cell division control protein 25	0.97	-	nuc	0		cytoplasm [IDA] plasma membrane [IDA]			1589
Q6NRL1 UniProt NPD GO	CENG2_XENLA	Centaurin-gamma 2	0.97	-	nuc	0	Cytoplasm (By similarity). Associates with the endocytic compartment (By similarity)				864
Q96P47 UniProt NPD GO	CENG3_HUMAN	Centaurin-gamma 3 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.97	-	nuc	0	Cytoplasm. In cells upon oxidative stress or in brains of Machado-Joseph disease patients, transloca ...				875
O43159 UniProt NPD GO	HUCE1_HUMAN	Cerebral protein 1	0.97	+	nuc	0	Nucleus; nucleolus				456
P53911 UniProt NPD GO	EAF7_YEAST	Chromatin modification-related protein EAF7 (ESA1-associated factor 7)	0.97	+	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA]			425
Q06337 UniProt NPD GO	VID21_YEAST	Chromatin modification-related protein VID21 (ESA1-associated factor 1) (Vacuolar import and degrada ...	0.97	-	nuc	0	Nucleus (Probable)	H4/H2A histone acetyltransferase complex [IPI]			982
Q22516 UniProt NPD GO	CHD3_CAEEL	Chromodomain helicase-DNA-binding protein 3 homolog (CHD-3)	0.97	+	nuc	0	Nucleus (Potential)				1787
Q6PDQ2 UniProt NPD GO	CHD4_MOUSE	Chromodomain helicase-DNA-binding protein 4 (CHD-4)	0.97	+	nuc	0	Nucleus (By similarity)				1915

You are viewing entries 901 to 950 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.